title: A prognostic DNA methylation signature for stage I non-small-cell lung cancer.
abstract: OBJECTIVE
  Non-small-cell lung cancer (NSCLC) is a tumor in which only small improvements in clinical outcome have been achieved. The issue is critical for stage I patients for whom there are no available biomarkers that indicate which high-risk patients should receive adjuvant chemotherapy. We aimed to find DNA methylation markers that could be helpful in this regard.
  
  
  METHODS
  A DNA methylation microarray that analyzes 450,000 CpG sites was used to study tumoral DNA obtained from 444 patients with NSCLC that included 237 stage I tumors. The prognostic DNA methylation markers were validated by a single-methylation pyrosequencing assay in an independent cohort of 143 patients with stage I NSCLC.
  
  
  RESULTS
  Unsupervised clustering of the 10,000 most variable DNA methylation sites in the discovery cohort identified patients with high-risk stage I NSCLC who had shorter relapse-free survival (RFS; hazard ratio [HR], 2.35; 95% CI, 1.29 to 4.28; P = .004). The study in the validation cohort of the significant methylated sites from the discovery cohort found that hypermethylation of five genes was significantly associated with shorter RFS in stage I NSCLC: HIST1H4F, PCDHGB6, NPBWR1, ALX1, and HOXA9. A signature based on the number of hypermethylated events distinguished patients with high- and low-risk stage I NSCLC (HR, 3.24; 95% CI, 1.61 to 6.54; P = .001).
  
  
  CONCLUSIONS
  The DNA methylation signature of NSCLC affects the outcome of stage I patients, and it can be practically determined by user-friendly polymerase chain reaction assays. The analysis of the best DNA methylation biomarkers improved prognostic accuracy beyond standard staging.
authors.affiliation: Juan Sandoval, Jesus Mendez-Gonzalez, F. Javier Carmona, Sergi Sayols, Sebastian Moran, Holger Heyn, Miguel Vizoso, Antonio Gomez, Montse Sanchez-Cespedes, and Manel Esteller, Bellvitge Biomedical Research Institute; Josefina Mora, Hospital de la Santa Creu i Sant Pau; Manel Esteller, University of Barcelona and Institucio Catalana de Recerca i Estudis Avançats, Barcelona; Miquel Taron and Rafael Rosell, Catalan Institute of Oncology, Badalona, Catalonia; Marina Pollan, Instituto de Salud Carlos III, Madrid; Maria J. Pajares and Luis M. Montuenga, University of Navarra; Wenceslao Torre, Clínica University de Navarra, Pamplona, Spain; Ernest Nadal, Guoan Chen, and David G. Beer, University of Michigan Medical School, Ann Arbor, MI; Yassen Assenov and Fabian Müller, Max Planck Institute, Saarbrücken, Germany; Christoph Bock, Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Lucia A. Muscarella, Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS) Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy; Triantafillos Liloglou, Michael Davies, and John K. Field, The University of Liverpool Cancer Research Centre, Liverpool, United Kingdom; Elisabeth Brambilla, Centre Hospitalier Universitaire A Michallon, Grenoble, France; Luca Roz, IRCCS Foundation National Cancer Institute, Milan; Marco Lo Iacono and Giorgio V. Scagliotti, University of Torino, Orbassano (Torino), Italy.
authors.forename: Juan
authors.initials: J
authors.lastname: Sandoval
authors.forename: Jesus
authors.initials: J
authors.lastname: Mendez-Gonzalez
authors.forename: Ernest
authors.initials: E
authors.lastname: Nadal
authors.forename: Guoan
authors.initials: G
authors.lastname: Chen
authors.forename: F Javier
authors.initials: FJ
authors.lastname: Carmona
authors.forename: Sergi
authors.initials: S
authors.lastname: Sayols
authors.forename: Sebastian
authors.initials: S
authors.lastname: Moran
authors.forename: Holger
authors.initials: H
authors.lastname: Heyn
authors.forename: Miguel
authors.initials: M
authors.lastname: Vizoso
authors.forename: Antonio
authors.initials: A
authors.lastname: Gomez
authors.forename: Montse
authors.initials: M
authors.lastname: Sanchez-Cespedes
authors.forename: Yassen
authors.initials: Y
authors.lastname: Assenov
authors.forename: Fabian
authors.initials: F
authors.lastname: Müller
authors.forename: Christoph
authors.initials: C
authors.lastname: Bock
authors.forename: Miquel
authors.initials: M
authors.lastname: Taron
authors.forename: Josefina
authors.initials: J
authors.lastname: Mora
authors.forename: Lucia A
authors.initials: LA
authors.lastname: Muscarella
authors.forename: Triantafillos
authors.initials: T
authors.lastname: Liloglou
authors.forename: Michael
authors.initials: M
authors.lastname: Davies
authors.forename: Marina
authors.initials: M
authors.lastname: Pollan
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Pajares
authors.forename: Wenceslao
authors.initials: W
authors.lastname: Torre
authors.forename: Luis M
authors.initials: LM
authors.lastname: Montuenga
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Brambilla
authors.forename: John K
authors.initials: JK
authors.lastname: Field
authors.forename: Luca
authors.initials: L
authors.lastname: Roz
authors.forename: Marco
authors.initials: M
authors.lastname: Lo Iacono
authors.forename: Giorgio V
authors.initials: GV
authors.lastname: Scagliotti
authors.forename: Rafael
authors.initials: R
authors.lastname: Rosell
authors.forename: David G
authors.initials: DG
authors.lastname: Beer
authors.forename: Manel
authors.initials: M
authors.lastname: Esteller
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000235:genetics*; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D016000:Cluster Analysis; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D018572:Disease-Free Survival; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D053208:Kaplan-Meier Estimate; D008175:Lung Neoplasms / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D008297:Male; D008875:Middle Aged; D009367:Neoplasm Staging; D020411:Oligonucleotide Array Sequence Analysis; D011379:Prognosis; D016016:Proportional Hazards Models; D059467:Transcriptome / Q000235:genetics*
chemical_list: D014408:Biomarkers, Tumor